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function [spike] = ft_spike_select(cfg, spike)
% FT_SPIKE_SELECT selects subsets of spikes, channels and trials from a
% spike structure.
% Use as
% [spike] = ft_spike_select(cfg, spike)
% The input SPIKE should be organised as the spike datatype (see
% Configurations:
% cfg.spikechannel = See FT_CHANNELSELECTION for details.
% cfg.trials = vector of indices (e.g., 1:2:10)
% logical selection of trials (e.g., [1010101010])
% 'all' (default), selects all trials
% cfg.latency = [begin end] in seconds
% 'maxperiod' (default), i.e., maximum period available
% 'minperiod', i.e., the minimal period all trials share
% 'prestim' (all t<=0)
% 'poststim' (all t>=0).
% Outputs:
% Spike structure with selections
% Copyright (C) 2012, Martin Vinck
% This file is part of FieldTrip, see
% for the documentation and details.
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% GNU General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <>.
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_preamble init
ft_preamble provenance spike
% control input spike structure
spike = ft_checkdata(spike,'datatype', 'spike', 'feedback', 'yes');
% get the default options
cfg.spikechannel = ft_getopt(cfg, 'spikechannel', 'all');
cfg.trials = ft_getopt(cfg, 'trials', 'all');
cfg.latency = ft_getopt(cfg, 'latency', 'maxperiod');
% ensure that the options are valid
cfg = ft_checkopt(cfg,'spikechannel',{'cell', 'char', 'double'});
cfg = ft_checkopt(cfg,'latency', {'char', 'ascendingdoublebivector'});
cfg = ft_checkopt(cfg,'trials', {'char', 'doublevector', 'logical'});
% select the desired channels
doAll = strcmp(cfg.spikechannel,'all');
cfg.spikechannel = ft_channelselection(cfg.spikechannel, spike.label);
[I,J] = unique(spike.label, 'first');
label = spike.label(J);
cfg.spikechannel = ft_channelselection(cfg.spikechannel, label);
spikesel = match_str(spike.label, cfg.spikechannel);
nUnits = length(spikesel);
if nUnits==0, error('no spikechannel selected by means of cfg.spikechannel');end
doAllTrials = strcmp(cfg.trials,'all');
doAllLatencies = strcmp(cfg.latency,'maxperiod');
% select the desired channels
if ~doAll
fprintf('Selecting channels\n');
try, spike.time = spike.time(spikesel); end
try, spike.trial = spike.trial(spikesel); end
try, spike.waveform = spike.waveform(spikesel); end
try, spike.timestamp = spike.timestamp(spikesel); end
try, spike.unit = spike.unit(spikesel); end
try, spike.fourierspctrm = spike.fourierspctrm(spikesel); end
try, spike.label = spike.label(spikesel); end
% select the desired trials
if ~isfield(spike,'trial') || ~isfield(spike,'trialtime') || ~isfield(spike,'time')
if ~doAllTrials
warning('spike structure does not contain trial, time or trialtime field, cannot select trials');
doSelection = ~strcmp(cfg.trials,'all');
cfg = trialselection(cfg,spike);
if doSelection
fprintf('Selecting trials\n');
nUnits = length(spike.trial);
for iUnit = 1:nUnits
spikesInTrial = ismember(spike.trial{iUnit},cfg.trials); % get spikes in trial
spike.trial{iUnit} = spike.trial{iUnit}(spikesInTrial);
spike.time{iUnit} = spike.time{iUnit}(spikesInTrial);
try, spike.timestamp{iUnit} = spike.timestamp{iUnit}(spikesInTrial); end
try, spike.waveform{iUnit} = spike.waveform{iUnit}(spikesInTrial); end
try, spike.unit{iUnit} = spike.unit{iUnit}(spikesInTrial); end
try, spike.fourierspctrm{iUnit} = spike.fourierspctrm{iUnit}(spikesInTrial,:,:); end
warning('No selection is performed on spike.trialtime and spike.sampleinfo');
% Note: .trialtime and .sampleinfo are explicitly left intact, as the
% relationship between trial number and trialtime becomes ambigious
% otherwise!
% select the desired latencies
if ~isfield(spike, 'trialtime') || ~isfield(spike,'time') || ~isfield(spike,'trial')
if ~doAllLatencies
warning('cannot select latencies as either .trialtime, .time or .trial is missing');
if ~strcmp(cfg.latency,'maxperiod') % otherwise, all spikes are selected
fprintf('Selecting on latencies\n');
begTrialLatency = spike.trialtime(cfg.trials,1);
endTrialLatency = spike.trialtime(cfg.trials,2);
cfg = latencyselection(cfg,begTrialLatency,endTrialLatency);
for iUnit = 1:nUnits
spikesInWin = spike.time{iUnit}>=cfg.latency(1) & spike.time{iUnit}<=cfg.latency(2); % get spikes in trial
spike.trial{iUnit} = spike.trial{iUnit}(spikesInWin);
spike.time{iUnit} = spike.time{iUnit}(spikesInWin);
try, spike.timestamp{iUnit} = spike.timestamp{iUnit}(spikesInWin); end
try, spike.waveform{iUnit} = spike.waveform{iUnit}(spikesInWin); end
try, spike.unit{iUnit} = spike.unit{iUnit}(spikesInWin); end
try, spike.fourierspctrm{iUnit} = spike.fourierspctrm{iUnit}(spikesInWin,:,:); end
% modify the trialtime
adjust = spike.trialtime(:,1)<=cfg.latency(1);
spike.trialtime(adjust,1) = cfg.latency(1);
adjust = spike.trialtime(:,2)>=cfg.latency(2);
spike.trialtime(adjust,2) = cfg.latency(2);
% FIXME: change sampleinfo field automatically again, for now remove.
try, spike = rmfield(spike,'sampleinfo'); end
% do the general cleanup and bookkeeping at the end of the function
ft_postamble previous spike
ft_postamble provenance spike
ft_postamble history spike
%%%%%%%%% SUB FUNCTIONS %%%%%%%%%
function [cfg] = latencyselection(cfg,begTrialLatency,endTrialLatency)
if strcmp(cfg.latency,'minperiod')
cfg.latency = [max(begTrialLatency) min(endTrialLatency)];
elseif strcmp(cfg.latency,'maxperiod')
cfg.latency = [min(begTrialLatency) max(endTrialLatency)];
elseif strcmp(cfg.latency,'prestim')
cfg.latency = [min(begTrialLatency) 0];
elseif strcmp(cfg.latency,'poststim')
cfg.latency = [0 max(endTrialLatency)];
function [cfg] = trialselection(cfg,spike)
% get the number of trials or change DATA according to cfg.trials
nTrials = size(spike.trialtime,1);
if strcmp(cfg.trials,'all')
cfg.trials = 1:nTrials;
elseif islogical(cfg.trials) || all(cfg.trials==0 | cfg.trials==1)
cfg.trials = find(cfg.trials);
cfg.trials = sort(cfg.trials(:));
if max(cfg.trials)>nTrials, error('maximum trial number in cfg.trials should not exceed length of spike.trialtime')
if isempty(cfg.trials), error('No trials were selected');